Population structure and genetic bottleneck in sweet cherry estimated with SSRs and the gametophytic self-incompatibility locus

Abstract

BackgroundDomestication and breeding involve the selection of particular phenotypes, limiting the genomic diversity of the population and creating a bottleneck. These effects can be precisely estimated when the location of domestication is established. Few analyses have focused on understanding the genetic consequences of domestication and breeding in fruit trees. In this study, we aimed to analyse genetic structure and changes in the diversity in sweet cherry Prunus avium L.ResultsThree subgroups were detected in sweet cherry, with one group of landraces genetically very close to the analysed wild cherry population. A limited number of SSR markers displayed deviations from the frequencies expected under neutrality. After the removal of these markers from the analysis, a very limited bottleneck was detected between wild cherries and sweet cherry landraces, with a much more pronounced bottleneck between sweet cherry landraces and modern sweet cherry varieties. The loss of diversity between wild cherries and sweet cherry landraces at the S-locus was more significant than that for microsatellites. Particularly high levels of differentiation were observed for some S-alleles.ConclusionsSeveral domestication events may have happened in sweet cherry or/and intense gene flow from local wild cherry was probably maintained along the evolutionary history of the species. A marked bottleneck due to breeding was detected, with all markers, in the modern sweet cherry gene pool. The microsatellites did not detect the bottleneck due to domestication in the analysed sample. The vegetative propagation specific to some fruit trees may account for the differences in diversity observed at the S-locus. Our study provides insights into domestication events of cherry, however, requires confirmation on a larger sampling scheme for both sweet cherry landraces and wild cherry.

Is the genetic diversity of small scattered forest tree populations at the southern limits of their range more prone to stochastic events? A wild cherry case study by microsatellite-based markers

“…The mean genetic diversity within populations (H e =0.740) was high and in agreement with the elevated microsatellite heterozygosity found in most tree species (Sanou et al 2005). In fact, it was higher than corresponding values from other studies in managed and unmanaged P. avium populations that originated from the central and northern extant wild cherry distribution range (France, Central Europe, UK; Mariette et al 2010;Stoeckel et al 2006;Vaughan et al 2007). Average allelic richness across loci was also high (AR=6.849), but lower than the mean values reported from SSR P. avium studies (Stoeckel et al 2006;Vaughan et al 2007;Mariette et al 2010).…”

“…Early domestication of Prunus has been indicated in Asia Minor since 7,000 BP (Behre 1978), and P. avium was apparently first cultivated in Greece since at least 2,300 BP according to Theophrastos (Hedrick 1915;Marshall 1954). It was introduced to western Europe by the Romans (Zohary and Hopf 2000), and there is accumulating evidence of multiple domestication events (Mariette et al 2010). The current species distribution presents its southeastern limits in Greece, forming small isolated populations.…”

Comparative population genomics reveals the domestication history of the peach,

“…The multiple of the ratio of the heterozygous SNPs in wild versus cultivated peach is 3.012, higher than that of two self-compatible species, soybean (1.552) [6] and rice (1.200) [9], and higher than that of two selfincompatible species, apple [38] and cherry [39] (Table S11 in Additional file 1). The decreased number of heterozygous SNPs in the cultivated group was a result of the change in the number of SNPs and the polymorphisms in intergenic regions during the domestication of the peach.…”

Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers

“…SSRs have been successfully used to identify cultivars and germplasm accessions in many fruits such as grape (Vitis sp.) (Cipriani et al 2010), sweet cherry (Mariette et al 2010), citrus (Gulsen and Roose 2001), peach (Aranzana et al 2010), and kiwifruit (Actinidia Lindl.) (Zhen et al 2004).…”